Contacts of the strand formed by residues 443 - 450 (chain A) in PDB entry 3HN3
Residue contacts within the protein are
derived with the CSU software (Sobolev V., Sorokine A.,
Prilusky J., Abola E.E. and Edelman M. (1999) Automated
analysis of interatomic contacts in proteins.
Bioinformatics, 15, 327-332). A
short description of the analytical approach
is given at the end of the page.
Note:
Non-standard 3 letter residue
codes indicate a heterogroup. To identify
and analyse, use LPC software
Legend:
Dist - nearest distance (Å) between atoms of two residues
Surf - contact surface area (Å2) between two residues
HB - hydrophilic-hydrophilic contact (hydrogen bond)
Arom - aromatic-aromatic contact
Phob - hydrophobic-hydrophobic contact
DC - hydrophobic-hydrophilic contact (destabilizing contact)
+/- - indicates presence/absence of a specific contacts
* - indicates residues forming contacts by their side chain
(including CA atoms)
Residues in contact with VAL 443 (chain A).
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Specific contacts
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Residue Dist Surf HB Arom Phob DC
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327A ARG* 2.9 14.0 + - - -
393A MET* 4.3 16.2 - - - -
403A VAL* 3.5 9.0 - - + +
405A ASP* 3.7 39.0 - - + +
437A ASP* 4.3 6.1 - - + +
440A HIS* 3.1 26.7 + - + +
442A ALA* 1.3 75.4 - - + +
444A VAL* 1.3 62.0 + - - +
445A MET 3.9 10.1 - - - +
446A TRP* 4.1 9.9 - - + -
477A ARG* 2.8 38.0 + - - +
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Residues in contact with VAL 444 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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288A TRP* 5.6 0.4 - - + -
327A ARG* 4.3 2.2 - - - +
329A VAL* 3.8 28.4 - - + +
336A PHE* 3.8 8.6 - - + -
338A ILE* 4.1 9.9 - - + -
345A PHE* 3.9 30.5 - - + -
402A VAL* 3.9 27.4 - - + -
403A VAL 3.0 17.5 + - - +
404A ILE* 5.0 0.2 - - + -
441A PRO 4.1 8.1 - - - +
442A ALA 3.6 9.6 - - - +
443A VAL* 1.3 75.9 - - - +
445A MET* 1.3 61.9 + - + +
477A ARG* 4.0 6.1 - - - +
478A PRO* 3.2 24.7 - - - +
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Residues in contact with MET 445 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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336A PHE* 4.3 7.4 - - + -
345A PHE* 4.8 1.1 - - + -
403A VAL 3.6 2.7 + - - +
404A ILE* 3.4 27.3 - - + -
405A ASP* 2.9 25.8 + - - -
443A VAL* 3.7 6.0 - - - +
444A VAL* 1.3 82.5 - - + +
446A TRP* 1.3 76.4 + - - +
477A ARG* 4.4 2.0 - - - +
478A PRO* 3.3 29.4 - - + +
479A VAL 4.6 0.7 - - - -
480A THR* 4.0 22.0 - - + -
498A VAL* 3.8 31.6 - - + -
500A CYS* 4.2 2.2 - - - -
537A ILE* 3.9 28.9 - - + -
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Residues in contact with TRP 446 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ILE* 4.7 0.2 - - - -
405A ASP* 3.5 40.4 - - + -
430A MET* 4.1 10.3 - - + -
433A VAL* 3.9 20.4 - - + -
434A VAL* 3.9 29.4 - - + -
437A ASP* 4.0 22.2 - - + -
438A LYS* 4.3 3.6 - - - -
443A VAL* 4.1 5.4 - - + -
445A MET* 1.3 75.7 - - - +
447A SER* 1.3 61.2 + - - +
470A THR* 3.8 29.1 - - + +
474A ASP* 2.9 36.2 + - + +
477A ARG* 3.5 27.8 - - + +
478A PRO 3.1 15.3 + - - +
479A VAL* 3.4 9.4 - - + -
480A THR* 2.8 29.8 + - - +
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Residues in contact with SER 447 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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404A ILE* 3.8 17.3 - - - -
405A ASP 3.0 8.8 + - - +
406A GLU* 2.7 36.6 + - - +
407A CYS* 3.1 26.3 + - - +
430A MET* 4.5 2.2 - - - +
445A MET 4.1 0.2 + - - -
446A TRP* 1.3 73.7 - - - +
448A VAL* 1.3 59.5 + - - +
449A ALA 3.3 13.7 + - - -
480A THR* 3.3 10.3 - - - -
481A PHE* 3.9 3.1 - - - -
482A VAL* 3.8 7.3 - - - +
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Residues in contact with VAL 448 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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407A CYS* 3.1 13.3 - - - -
409A GLY* 3.9 0.2 - - - -
426A HIS* 2.7 29.8 + - - +
430A MET* 4.2 9.6 - - + -
447A SER* 1.3 74.2 - - - +
449A ALA* 1.3 61.3 + - - +
463A LEU* 4.1 15.5 - - + -
466A VAL* 3.6 22.9 - - + -
467A ILE* 3.9 16.6 - - + -
470A THR* 3.8 17.3 - - - +
479A VAL* 3.6 28.0 - - + -
480A THR 3.0 13.6 + - - +
481A PHE* 3.8 10.5 - - + -
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Residues in contact with ALA 449 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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406A GLU* 4.4 4.7 - - - +
409A GLY* 3.1 17.9 - - - +
412A LEU* 4.7 2.0 - - + -
426A HIS* 4.7 3.6 - - + -
447A SER* 3.3 12.3 + - - -
448A VAL* 1.3 83.8 - - - +
450A ASN* 1.3 62.5 + - - +
452A PRO* 4.1 14.4 - - + -
463A LEU* 4.1 17.3 - - + -
481A PHE* 3.9 12.4 - - + +
482A VAL* 2.9 25.1 + - - +
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Residues in contact with ASN 450 (chain A).
Click here for Legend to table.
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Specific contacts
---------------------------
Residue Dist Surf HB Arom Phob DC
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382A ARG* 2.9 19.7 + - - +
385A HIS* 3.3 27.0 + - - +
406A GLU* 3.6 17.7 - - - +
409A GLY 2.9 10.0 + - - +
410A VAL* 3.8 33.0 - - + +
411A GLY 4.1 1.7 + - - -
449A ALA* 1.3 74.7 - - - +
451A GLU* 1.3 89.3 + - - +
452A PRO* 3.3 1.9 - - - +
482A VAL* 3.3 16.2 - - - +
502A ASN* 3.5 6.4 + - - -
540A GLU* 3.5 1.6 + - - +
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A short description of the
analytical approach
The contact analysis used in this page
is based upon the approach
developed in:
Sobolev V., Wade R.C., Vriend G.
and Edelman M. PROTEINS (1996)
25, 120-129.
Contact legitimacy depends on the hydrophobic-hydrophilic
properties of the contacting atoms. In order to
define it, for each inter-atomic contact,
eight atom classes have been introduced:
I Hydrophilic - N and O that can donate and accept hydrogen bonds
(e.g., oxygen of hydroxyl group of Ser. or Thr)
II Acceptor - N or O that can only accept a hydrogen bond
III Donor - N that can only donate a hydrogen bond
IV Hydrophobic - Cl, Br, I and all C atoms that are not in
aromatic rings and do not have a covalent bond to
a N or O atom
V Aromatic - C in aromatic rings irrespective of any other
bonds formed by the atom
VI Neutral - C atoms that have a covalent bond to at least one
atom of class I or two or more atoms from class II
or III; atoms; S, F, P, and metal atoms in all cases
VII Neutral-donor - C atoms that have a covalent bond with only one
atom of class III
VIII Neutral-acceptor - C atoms that have a covalent bond with only
one atom of class II
For each pair of contacts the state of legitimacy
is shown below:
Legend:
+, legitimate
-, illegitimate
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Atomic class I II III IV V VI VII VIII
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I (Hydrophilic) + + + - + + + +
II (Acceptor) + - + - + + + -
III (Donor) + + - - + + - +
IV (Hydrophobic) - - - + + + + +
V (Aromatic) + + + + + + + +
VI (Neutral) + + + + + + + +
VII (Neutral-donor) + + - + + + - +
VIII (Neutral-acceptor) + - + + + + + -
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Warning!
Atom classes for heterogroups are automatically
assigned based on the atomic coordinates. However, in
three cases (see below) the automatic assignment
is currently ambiguous. In these
cases, the user is advised to manually analyse
the full list of contacts using
LPC software.
1. Carbon atoms belonging to a 4-, 5- or 6-member ring are
considered "aromatic" (Class V) if the ring is approximately
planar, and "hydrophobic" (Class IV) or "neutral" (Classes
VI, VII, VIII) if the ring is non-planar.
2. The oxygen atom of a carbonyl or hydroxy group is considered
"hydroxy" (Class I) if the CO bond is longer than 1.29 Å, and
"carbonyl" (Class II) if shorter.
3. All nitrogen atoms are considered "hydrophilic" (Class I).
Please E-mail any
questions and/or suggestions concerning this page to
Vladimir.Sobolev@weizmann.ac.il